Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF3587 Psest_3654 succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__psRCH2:GFF3587 Length = 488 Score = 554 bits (1427), Expect = e-162 Identities = 270/481 (56%), Positives = 361/481 (75%), Gaps = 3/481 (0%) Query: 45 DLLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKE 102 DLLR +++ G W A +++PA+G +G V + G E R A+ AA A +W+ Sbjct: 9 DLLRQTAYLNGEWCEADSGARTEIFNPATGELIGAVPNMGRGETRRAIEAAQAAQPAWRA 68 Query: 103 ISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRV 162 ++ KER++ LR+WY+LM++N+++LA+I+TAE GKPL EA+GE+ Y+A FLEWF+EE +R+ Sbjct: 69 LTAKERAARLRRWYELMLENQEDLARIMTAEQGKPLAEARGEVAYAASFLEWFAEEGKRL 128 Query: 163 YGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTP 222 YGD+I A DKR LV K+PVGV + ITPWNFPSAMITRK G ALAAGC +V+KPA TP Sbjct: 129 YGDVIPAHAGDKRILVQKEPVGVTAAITPWNFPSAMITRKAGPALAAGCAMVLKPAPQTP 188 Query: 223 YSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLH 282 +SALALA LA +AGIP G+ +VI ++EVG LC +P+V K+SFTGSTA G L+ Sbjct: 189 FSALALAALAERAGIPAGLLSVITADAATSREVGAELCENPIVRKLSFTGSTAVGIKLMQ 248 Query: 283 HAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHD 342 A ++K++S+ELGG APFIVFD A++D AV GAM SK+RNAGQTCVC+NR VQ GI+D Sbjct: 249 QCAPTLKKLSLELGGNAPFIVFDDADLDAAVEGAMISKYRNAGQTCVCANRIYVQDGIYD 308 Query: 343 SFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQ 402 +FV K + A+ + L+VGNG EEG T GPLI+ AV KV++H+ DA+ KGAT++ GGK H Sbjct: 309 AFVDKLSAAVAR-LKVGNGAEEGVTTGPLIDAAAVAKVQRHLQDALDKGATLLAGGKPHA 367 Query: 403 SGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQD 462 GGNFFEPTL+ VT +M EETFGP+AP+ +F E+E + AN + GLA YFY++D Sbjct: 368 LGGNFFEPTLVGGVTSEMAVAREETFGPLAPLFRFRDEDEVIRQANDTEFGLAAYFYARD 427 Query: 463 PAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGG 522 ++++RVAE LE GMVG+N G+IS+ PFGG+K SGLGREGSKYG+DEY+E+KY+C GG Sbjct: 428 LSRVFRVAEALEYGMVGINTGVISTEVAPFGGMKASGLGREGSKYGLDEYVEIKYLCLGG 487 Query: 523 L 523 + Sbjct: 488 I 488 Lambda K H 0.318 0.135 0.400 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 643 Number of extensions: 22 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 523 Length of database: 488 Length adjustment: 34 Effective length of query: 489 Effective length of database: 454 Effective search space: 222006 Effective search space used: 222006 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory